Exploration of fishing scenarios

This workflow must run after the workflow: Resident killer whale-chinook salmon interactions. The interaction workflows generates a PostWorkspace file, this is a zip file and it is an R Workspace that transfers values from the Resident killer whale-chinook salmon interactions (main) workflow to the Exploration of fishing scenario (post-processing) workflow.

This workflow merges statistical inference derived from linkages between RKW vital rates (survival probability and fecundity rates) and chinook salmon abundance with demographic perturbation analysis and population viability analysis to address some of the pressing questions that have recently engaged the efforts of scientists and managers interested in: (1) the role of chinook salmon abundance in the population dynamics of RKW; and (2) how RKW population viability is expected to respond to changes in chinook mortality owing to harvest.

This workflow can be used to analyze interactions between chinook salmon abundance from specific stock aggregates and killer whale vital rates, the effect of these interactions on killer whale population growth, and the exploration of Chinook salmon fishing scenarios on killer whale population growth and short term projections of population size. See necessary input data.

To run this workflow in Taverna Workbench Biodiversity 2.5 requires an Rserve installation with the popbio, lattice, betareg, Formula and R.utils packages installed.

Data Inputs (5)

ER_Indicators_R (text/csv)

This file shows the exploitation rate (ER) indicator stocks used to represent exploitation-rate time series with terminal-run time series of Chinook salmon aggregates.

Term_Run_R (text/csv)

Description:

This file contains the time series of terminal run for each of the ER indicator stocks.

TRE_HR_R (text/csv)

Description:

This file contains the time series of terminal run equivalent (TRE) ocean harvest rates of ER indicator stocks.

Chinook salmon is an anadromous and semelparous species that spend 1-5 years in the ocean before returning to their natal streams to spawn. For the exploration of fishing scenarios where changes in terminal run size occur as a result of changes in ocean (i.e. pre-terminal) harvest rates, terminal run equivalents (TRE) were used to account for the fact that only a portion of the fish not caught in ocean fisheries in a given year is expected to become part of the terminal run according to their maturation rates (MR), which are time variant and stock specific. Age-2 Chinook were not included in this equation because RKW prey mostly on age-3 and older Chinook. TREs were then used to compute both proportional increases in terminal run size in the absence of pre-terminal (i.e. ocean) fishing and the terminal run scalars resulting from a specified change in ocean harvest rates in exploitation rate indicator stocks. These scalars were then used to calculate changes in terminal run of a stock of interest (more details in Vélez-Espino et al. In press).

TRE_R (text/csv)

Description:

This file contains the time series of terminal run equivalents (TREs) of all ER indicator stocks.

Workspace (application/zip)

Description:

An R Workspace that transfers values from the Resident killer whale-chinook salmon interactions (main) workflow to the Exploration of fishing scenario (post-processing) workflow. The zip file must be provided as an input to the post-processing workflow in order for it to have access to values generated in the main workflow. Therefore, take in account the input values used to run the main workflow.

Parameter Inputs (5)

MLT (text/plain)

Description:

This is a user-defined inverse multiplier for the harvest rate (HR) that affects the stock aggregates directly. MLT is inversely proportional to HRs but directly proportional to killer whale vital rates. MLT = 0.0 is used to maximize HRs. MLT values between 1.0 and 2.0 are used to represent increments in ocean abundance proportional to percent reductions in HRs.

StockAggr (text/plain)

Description:

The stock aggregate, with abundance represented as terminal run (TR), is user defined from the list of significant stocks from the regression and elasticity analyses. The user needs to see “Elasticities of Interaction Method Matrix Pert._Population_(Beta Regressions).pdf” or “Elasticity of Interactions_Population.csv” to select relevant stock aggregates for further analysis.

Example value:

FEPS_TR_1

StockAggrOA (text/plain)

Description:

The stock aggregate, with abundance represented as ocean abundance (OA), is user defined from the list of significant stocks from the regression and elasticity analyses. The user needs to see “Elasticities of Interaction Method Matrix Pert._Population_(Beta Regressions).pdf” or “Elasticity of Interactions_Population.csv” to select relevant stock aggregates for further analysis.

Example value:

CW_OA_2

UseFImpacts (text/plain)

Description:

Instead of ocean abundance, the user can select time series of fishery impacts to run the analyses. In this case, the interaction would be between killer whale vital rates and fishing impacts rather than Chinook salmon ocean abundance. Choose “FALSE” to conduct analyses at the ocean abundance level.

Example value:

FALSE

Outputs (1)

Result Outputs (1)

zipFile (application/zip)

Description:

Zip file with the results of workflow.
Results when a run is done with the defaults inputs (see tutorial).